DSBS analyzer is a pipeline to analyzing Double Strand Bisulfite Sequencing data, which could simultaneously identify SNVs and evaluate DNA methylation levels in a single base resolution. In DSBS, bisulfite-converted Watson strand and reverse complement of bisulfite-converted Crick strand derived from the same double-strand DNA fragment were sequenced in read 1 and read 2, and aligned to the same position on reference genome. By simultaneous analyzing the sequence of read 1 and read 2, the sequence and DNA methylation state of DNA fragment could be deduced.
python3 DSBS_analyzer.py --config DSBS.config -a /data_path/*_1.fq.gz -b /data_path/*_2.fq.gz -o /outdir &
python3 DSBS_analyzer.py
m m
| |
AGCTACGT bisulfite treat --> A G {T} TACGT AGTTACGT
||||||||-------------------->| | | | |||||
TCGATGCA (C>T) --> T {T} G ATGCA AACTAGCT
| |
m m
C>T 1) bisulfite conversion ?
2) mutation ?
3) sequencing errors ?
usage: DSBS_analyzer.py [-h] [--config CONFIG] -a [FQ1 [FQ1 ...]] -b
[FQ2 [FQ2 ...]] [-r REF]
[-k [KNOWNSITES [KNOWNSITES ...]]] [-d DEPTH]
[-q CLEANQUALITY] [--gapsize GAPSIZE] [--fastquniq]
[--remove_tmp] [--bissnp] [-t CPU] [--pp PP] -o
OUTDIR [--qsub]
-h, --help show this help message and exit
--config CONFIG config file
-a [FQ1 [FQ1 ...]], --fq1 [FQ1 [FQ1 ...]]
Fastq1(s), Space separation
-b [FQ2 [FQ2 ...]], --fq2 [FQ2 [FQ2 ...]]
Fastq2(s), Space separation
-r REF, --ref REF refrence
-k [KNOWNSITES [KNOWNSITES ...]], --knownsites [KNOWNSITES [KNOWNSITES ...]]
knownsites
-d DEPTH, --depth DEPTH
the minimum depth , default is 4
-q CLEANQUALITY, --cleanquality CLEANQUALITY
quality when clening the fastq
--gapsize GAPSIZE the size of insert or del, default is 3
--fastquniq rmdup fastq before cleanning fastq
--remove_tmp rm temp file
--bissnp bisSNP
-t CPU, --cpu CPU thread, default is 20
--pp PP 1,execute ,0,skip. 1)qualimap, 2)clean, 3)align,
4)dealBam, 5)call mutation and methylation , default 11111
-o OUTDIR, --outdir OUTDIR
outdir
--qsub use qsub
cat DSBS.config
Here is the example of config file which configured the path of softwares and databases and software operating environment. Y For those necessary softwares and databases, you are on your own. It is important to note that each software needs to have execute permission(chmod a+x soft).
#soft
java:/public/soft/jdk1.8.0_111/bin/java:soft
java1.6:/public/soft/jdk1.7.0_45/bin/java:soft
python3:/public/soft/python3:soft
fastqc:/public/soft/fastqc:soft
qualimap:/public/soft/qualimap_v2.2.1/qualimap:soft
#clean,rmdup
fastuniq:/public/soft/FastUniq/fastuniq:soft
cutadapt:/public/soft/cutadapt-1.8.1/bin/cutadapt:soft
filter_fq:/public/soft/filter_fq.py:soft
stdmap_awk:/public/soft/stdmap.awk:soft
diffmap_awk:/public/soft/diffmap.awk:soft
bsmap:/public/soft/bsmap2.7/bsmap:soft
bissnp:/public/soft/BisSNP/BisSNP-0.82.2.jar:soft
#qsub
job_sub_py_2:/public/soft/job_sub_py_2.py:soft
#index, sort, merge, split
samtools:/public/soft/samtools-1.8/samtools:soft
picard:/public/soft/picard-2.17.3/picard.jar:soft
#call SNP and methy
DSBS:/public/soft/DSBS.py:soft
#resource
refDir:/public/database/hg19/:resource
ref:/public/database/hg19/hg19.fa:resource
1000G_omni:/public/database/1000G_omni2.5.hg19.sites.vcf:resource
1000G_phase1:/public/database/1000G_phase1.snps.high_confidence.hg19.sites.vcf:resource
dbsnp:/public/database/dbsnp_138.hg19.vcf:resource
dbsnp_gz:/public/database/dbsnp_138.hg19.vcf.gz:resource
hapmap:/public//database/hapmap_3.3.hg19.sites.vcf:resource
DSBS depends on
python DSBS.py example.bam -g chr1.fa -d dbsnp138.vcf.gz --chr chr1 -o outdir -q
One time only, it is necessary to index a reference sequence and the dbsnp file。 The commands:
bgzip dbsnp_138.hg19.vcf
tabix -s 1 -b 2 dbsnp_138.hg19.vcf.gz (tabix -s 1 -b 2 -p vcf dbsnp_138.hg19.vcf.gz )
python DSBS.py
usage: DSBS.py [-h] [-v] [--maxDistance MAXDISTANCE] [--maxLen MAXLEN]
[--mixLen MIXLEN] [--mixReadQual MIXREADQUAL]
[--mixReadQualN MIXREADQUALN] [--maxN MAXN]
[--maxSeqErr MAXSEQERR] [--maxSnp MAXSNP] [--maxIndel MAXINDEL]
[--maxBp MAXBP] [--maxMut MAXMUT] [--minQual MINQUAL]
[--minVaf MINVAF] [--secAlign] [--debug] [-q] [-c COVERAGE]
[-p CPU] [-o OUTDIR] -g GENOMEFILE -d DBSNP [--Chr CHR]
bamFile
positional arguments:
bam input BAM file
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
--maxDistance MAXDISTANCE the maxmum distance of the start postions of the
paired reads in reference genome, default is 50
--maxLen MAXLEN the maxmum length of a read, default is 200
--minLen MINLEN the minimum length of a read, default is 50
--minReadQual MINREADQUAL the minimum quality for assessing the read
overall qualities, default is 20
--minReadQualN MINREADQUALN the minimum ratio which quality is greater than
the minReadQual, default is 0.6
--maxN MAXN the maxmum number of N within a read, default is 5
--maxSeqErr MAXSEQERR the maxmum number of sequencing errors within a paired
reads, default is 10
--maxSnp MAXSNP the maxmum number of snp within a paired reads,
default is 5
--maxIndel MAXINDEL the maxmum number of indel within a paired reads,
default is 1
--maxBp MAXBP a certain range for allowing the currence of certain
mutation ,default is 50
--maxMut MAXMUT the maxmum number of allowing the currence of
mutation within a certain range ,default is 3
--minQual MINQUAL the minimum quality for call Variation, default is 20
--minVaf MINVAF the minimum value of allele, default is 0.5
--window WINDOW ignoring the snps in a certain range of a indel, the
range is 5bp
--minCoverage MINCOVERAGE coverage or minimum number of reads desired,
default is 8
--maxCoverage MAXCOVERAGE coverage or maxmum number of reads desired,
default is 500
--strand only consider the correct comparison direction,
read1=++ && read2=-- || read1=-+ && read2=+-
--secAlign consider non-optimal alignments
--CpG output CpG
--CHG output CHG
--CHH output CHH
--debug dubug mode
-q, --quite quiet mode
-p CPU, --cpu CPU the number of working threads, default is 50
-o OUTDIR, --outDir OUTDIR the outDir
-g GENOMEFILE, --genomeFile GENOMEFILE
the chromosome reference fasta
-d DBSNP, --dbsnp DBSNP the dbsnp file
--Chr CHR chromosome
python3 DSBS.py chr1.merge.sorted.rmdup.realigned.recal.bam --maxBp 50 --minVaf 0.1 -q -p 40 -o outdir -g chr1.fa --Chr chr1 -d dbsnp_138.hg19.vcf.gz --secAlign
use job_sub_py_2.py which based on PBS to deliver the jobs
for i in {1..22} X Y M; do python3 job_sub_py_2.py --jobname chr$i --cpu 2 --work "python3 /public/soft/DSBS.py /datapath/chr$i.merge.sorted.rmdup.realigned.recal.bam --maxBp 50 --minVaf 0.1 -q --cpu 40 -o /outdir -g ~/public/database/hg19/chr$i.fa --Chr chr$i -d /public/database/dbsnp_138.hg19.vcf.gz " done
Contributions and suggestions for new features are welcome, as are bug reports! Please create a new issue for any of these, including example reports where possible.
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